What is the purpose of these templates. Are they actually in production? They say to never modify - in which case they may need protection - but really shouldn't system type messages be in the mediawiki space?
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It doesn't say never to modify the templates. They are expected to be customized on a per-site basis.
The ones that say that (e.g. https://en.wikipedia.org/wiki/Template:Archive_for_converted_LQT_page, "This page is an archived LiquidThreads page. Do not edit the contents of this page.") mean to never modify the archive page (for the same reason you shouldn't modify any ordinary archive page).
@Quiddity, we can definitely clarify the text here for future wikis if that helps.
And, yes, they are used in production on some wikis (which depends on which features are used on each wiki).
The name is in MW space, but normally that wouldn't need to be changed.